@vitessce/neuroglancer 3.9.5 → 3.9.7

package/dist-tsc/data-hook-ng-utils.d.ts

@@ -1,22 +1,14 @@
-export function extractDataTypeEntities(loaders: any, dataset: any, dataType: any): {
-    key: any;
-    type: string;
-    fileUid: any;
-    layout: string;
-    url: any;
-    source: string | undefined;
-    name: any;
-    dimensions: {
-        x: [number, "nm"];
-        y: [number, "nm"];
-        z: [number, "nm"];
-    };
-    position: any[];
-    projectionOrientation: any[];
-    projectionScale: any;
-    crossSectionScale: any;
-}[];
-export function useExtractOptionsForNg(loaders: any, dataset: any, dataType: any): any[];
+/**
+   * Normalize dimensionX/Y/Z to nanometers.
+   * @param {object} opts
+   * @returns {{ x:[number,'nm'], y:[number,'nm'], z:[number,'nm'] }}
+   */
+export function normalizeDimensionsToNanometers(opts: object): {
+    x: [number, "nm"];
+    y: [number, "nm"];
+    z: [number, "nm"];
+};
+export function toNgLayerName(dataType: any, layerScope: any, channelScope?: null): string;
 /**
  * Get the parameters for NG's viewerstate.
  * @param {object} loaders The object mapping
@@ -29,12 +21,18 @@ export function useExtractOptionsForNg(loaders: any, dataset: any, dataType: any
 /**
  * @returns [viewerState]
  */
-export function useNeuroglancerViewerState(loaders: any, dataset: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): any[];
+export function useNeuroglancerViewerState(theme: any, segmentationLayerScopes: any, segmentationChannelScopesByLayer: any, segmentationLayerCoordination: any, segmentationChannelCoordination: any, obsSegmentationsUrls: any, obsSegmentationsData: any, pointLayerScopes: any, pointLayerCoordination: any, obsPointsUrls: any, obsPointsData: any, pointMultiIndicesData: any): any;
 export namespace DEFAULT_NG_PROPS {
     let layout: string;
     let position: number[];
     let projectionOrientation: number[];
     let projectionScale: number;
     let crossSectionScale: number;
+    namespace dimensions {
+        let x: (string | number)[];
+        let y: (string | number)[];
+        let z: (string | number)[];
+    }
+    let layers: never[];
 }
 //# sourceMappingURL=data-hook-ng-utils.d.ts.map

package/dist-tsc/data-hook-ng-utils.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"data-hook-ng-utils.d.ts","sourceRoot":"","sources":["../src/data-hook-ng-utils.js"],"names":[],"mappings":"AAgDA;;;;KAIK;AACL,sDAHa,MAAM,GACJ;IAAE,CAAC,EAAC,CAAC,MAAM,EAAC,IAAI,CAAC,CAAC;IAAC,CAAC,EAAC,CAAC,MAAM,EAAC,IAAI,CAAC,CAAC;IAAC,CAAC,EAAC,CAAC,MAAM,EAAC,IAAI,CAAC,CAAA;CAAE,CA+BnE;AAED,2FAQC;AAED;;;;;;;;GAQG;AACH;;GAEG;AACH,yXAiJC"}

package/dist-tsc/data-hook-ng-utils.js

@@ -1,15 +1,23 @@
-import { useMemo } from 'react';
 import { DataType } from '@vitessce/constants-internal';
+import { cloneDeep } from 'lodash-es';
+import { useMemoCustomComparison, customIsEqualForInitialViewerState } from './use-memo-custom-comparison.js';
+import { getPointsShader } from './shader-utils.js';
 export const DEFAULT_NG_PROPS = {
     layout: '3d',
     position: [0, 0, 0],
     projectionOrientation: [0, 0, 0, 1],
     projectionScale: 1024,
     crossSectionScale: 1,
+    dimensions: {
+        x: [1, 'nm'],
+        y: [1, 'nm'],
+        z: [1, 'nm'],
+    },
+    layers: [],
 };
 function toPrecomputedSource(url) {
     if (!url) {
-        return undefined;
+        throw new Error('toPrecomputedSource: URL is required');
     }
     return `precomputed://${url}`;
 }
@@ -36,8 +44,8 @@ function isInNanometerRange(value, unit, minNm = 1, maxNm = 100) {
    * @param {object} opts
    * @returns {{ x:[number,'nm'], y:[number,'nm'], z:[number,'nm'] }}
    */
-function normalizeDimensionsToNanometers(opts) {
-    const { dimensionUnit, dimensionX, dimensionY, dimensionZ } = opts;
+export function normalizeDimensionsToNanometers(opts) {
+    const { dimensionUnit, dimensionX, dimensionY, dimensionZ, ...otherOptions } = opts;
     if (!dimensionUnit || !dimensionX || !dimensionY || !dimensionZ) {
         console.warn('Missing dimension info');
     }
@@ -48,70 +56,25 @@ function normalizeDimensionsToNanometers(opts) {
         console.warn('Dimension was converted to nm units');
     }
     return {
-        x: xNm ? [dimensionX, dimensionUnit] : [1, 'nm'],
-        y: yNm ? [dimensionY, dimensionUnit] : [1, 'nm'],
-        z: zNm ? [dimensionZ, dimensionUnit] : [1, 'nm'],
+        // The dimension-related fields are formatted differently in the fileDef.options
+        // vs. what the viewerState expects.
+        dimensions: {
+            x: xNm ? [dimensionX, dimensionUnit] : [1, 'nm'],
+            y: yNm ? [dimensionY, dimensionUnit] : [1, 'nm'],
+            z: zNm ? [dimensionZ, dimensionUnit] : [1, 'nm'],
+        },
+        // The non-dimension-related options can be passed through without modification.
+        ...otherOptions,
     };
 }
-export function extractDataTypeEntities(loaders, dataset, dataType) {
-    const datasetEntry = loaders?.[dataset];
-    const internMap = datasetEntry?.loaders?.[dataType];
-    if (!internMap || typeof internMap.entries !== 'function')
-        return [];
-    return Array.from(internMap.entries()).map(([key, loader]) => {
-        const url = loader?.url ?? loader?.dataSource?.url ?? undefined;
-        const fileUid = key?.fileUid
-            ?? loader?.coordinationValues?.fileUid
-            ?? undefined;
-        const { position, projectionOrientation, projectionScale, crossSectionScale } = loader?.options ?? {};
-        const isPrecomputed = loader?.fileType.includes('precomputed');
-        if (!isPrecomputed) {
-            console.warn('Filetype needs to be precomputed');
-        }
-        return {
-            key,
-            type: 'segmentation',
-            fileUid,
-            layout: DEFAULT_NG_PROPS.layout,
-            url,
-            source: toPrecomputedSource(url),
-            name: fileUid ?? key?.name ?? 'segmentation',
-            // For precomputed: nm is the unit used
-            dimensions: normalizeDimensionsToNanometers(loader?.options),
-            // If not provided, no error, but difficult to see the data
-            position: Array.isArray(position) && position.length === 3
-                ? position : DEFAULT_NG_PROPS.position,
-            // If not provided, will have a default orientation
-            projectionOrientation: Array.isArray(projectionOrientation)
-                && projectionOrientation.length === 4
-                ? projectionOrientation : DEFAULT_NG_PROPS.projectionOrientation,
-            projectionScale: Number.isFinite(projectionScale)
-                ? projectionScale : DEFAULT_NG_PROPS.projectionScale,
-            crossSectionScale: Number.isFinite(crossSectionScale)
-                ? crossSectionScale : DEFAULT_NG_PROPS.crossSectionScale,
-        };
-    });
-}
-export function useExtractOptionsForNg(loaders, dataset, dataType) {
-    const extractedEntities = useMemo(() => extractDataTypeEntities(loaders, dataset, dataType), [loaders, dataset, dataType]);
-    const layers = useMemo(() => extractedEntities
-        .filter(t => t.source)
-        .map(t => ({
-        type: t.type,
-        source: t.source,
-        segments: [],
-        name: t.name || 'segmentation',
-    })), [extractedEntities]);
-    const viewerState = useMemo(() => ({
-        dimensions: extractedEntities[0]?.dimensions,
-        position: extractedEntities[0]?.position,
-        crossSectionScale: extractedEntities[0]?.crossSectionScale,
-        projectionOrientation: extractedEntities[0]?.projectionOrientation,
-        projectionScale: extractedEntities[0]?.projectionScale,
-        layers,
-        layout: extractedEntities[0].layout,
-    }));
-    return [viewerState];
+export function toNgLayerName(dataType, layerScope, channelScope = null) {
+    if (dataType === DataType.OBS_SEGMENTATIONS) {
+        return `obsSegmentations-${layerScope}-${channelScope}`;
+    }
+    if (dataType === DataType.OBS_POINTS) {
+        return `obsPoints-${layerScope}`;
+    }
+    throw new Error(`Unsupported data type: ${dataType}`);
 }
 /**
  * Get the parameters for NG's viewerstate.
@@ -125,6 +88,111 @@ export function useExtractOptionsForNg(loaders, dataset, dataType) {
 /**
  * @returns [viewerState]
  */
-export function useNeuroglancerViewerState(loaders, dataset, isRequired, coordinationSetters, initialCoordinationValues, matchOn) {
-    return useExtractOptionsForNg(loaders, dataset, DataType.OBS_SEGMENTATIONS, matchOn);
+export function useNeuroglancerViewerState(theme, segmentationLayerScopes, segmentationChannelScopesByLayer, segmentationLayerCoordination, segmentationChannelCoordination, obsSegmentationsUrls, obsSegmentationsData, pointLayerScopes, pointLayerCoordination, obsPointsUrls, obsPointsData, pointMultiIndicesData) {
+    const viewerState = useMemoCustomComparison(() => {
+        let result = cloneDeep(DEFAULT_NG_PROPS);
+        // ======= SEGMENTATIONS =======
+        // Iterate over segmentation layers and channels.
+        segmentationLayerScopes.forEach((layerScope) => {
+            const layerCoordination = segmentationLayerCoordination[0][layerScope];
+            const channelScopes = segmentationChannelScopesByLayer[layerScope] || [];
+            const layerData = obsSegmentationsData[layerScope];
+            const layerUrl = obsSegmentationsUrls[layerScope]?.[0]?.url;
+            if (layerUrl && layerData) {
+                const { spatialLayerVisible, } = layerCoordination || {};
+                channelScopes.forEach((channelScope) => {
+                    const channelCoordination = segmentationChannelCoordination[0]?.[layerScope]?.[channelScope];
+                    const { spatialChannelVisible, } = channelCoordination || {};
+                    result = {
+                        ...result,
+                        layers: [
+                            ...result.layers,
+                            {
+                                type: 'segmentation',
+                                source: toPrecomputedSource(layerUrl),
+                                segments: [],
+                                name: toNgLayerName(DataType.OBS_SEGMENTATIONS, layerScope, channelScope),
+                                visible: spatialLayerVisible && spatialChannelVisible, // Both layer and channel
+                                // visibility must be true for the layer to be visible.
+                                // TODO: update this to extract specific properties from
+                                // neuroglancerOptions as needed.
+                                ...(layerData.neuroglancerOptions ?? {}),
+                            },
+                        ],
+                    };
+                });
+            }
+        });
+        // ======= POINTS =======
+        // Iterate over point layers.
+        pointLayerScopes.forEach((layerScope) => {
+            const layerCoordination = pointLayerCoordination[0][layerScope];
+            const layerData = obsPointsData[layerScope];
+            const layerUrl = obsPointsUrls[layerScope]?.[0]?.url;
+            const featureIndex = pointMultiIndicesData[layerScope]?.featureIndex;
+            if (layerUrl && layerData) {
+                const { spatialLayerVisible, spatialLayerOpacity, obsColorEncoding, spatialLayerColor, featureSelection, featureFilterMode, featureColor, } = layerCoordination || {};
+                // Dynamically construct the shader based on the color encoding
+                // and other coordination values.
+                const shader = getPointsShader({
+                    theme,
+                    featureIndex,
+                    spatialLayerOpacity,
+                    obsColorEncoding,
+                    spatialLayerColor,
+                    featureSelection,
+                    featureFilterMode,
+                    featureColor,
+                    featureIndexProp: layerData.neuroglancerOptions?.featureIndexProp,
+                    pointIndexProp: layerData.neuroglancerOptions?.pointIndexProp,
+                });
+                result = {
+                    ...result,
+                    layers: [
+                        ...result.layers,
+                        {
+                            type: 'annotation',
+                            source: {
+                                url: toPrecomputedSource(layerUrl),
+                                subsources: {
+                                    default: true,
+                                },
+                                enableDefaultSubsources: false,
+                            },
+                            tab: 'annotations',
+                            shader,
+                            name: toNgLayerName(DataType.OBS_POINTS, layerScope),
+                            visible: spatialLayerVisible,
+                            // Options from layerData.neuroglancerOptions
+                            // like projectionAnnotationSpacing:
+                            projectionAnnotationSpacing: layerData.neuroglancerOptions
+                                ?.projectionAnnotationSpacing ?? 1.0,
+                        },
+                    ],
+                    // TODO: is this needed?
+                    // The selected layer here will overwrite anything
+                    // that was previously specified.
+                    selectedLayer: {
+                        // size: ? // TODO:  is this needed?
+                        layer: toNgLayerName(DataType.OBS_POINTS, layerScope),
+                    },
+                };
+            }
+        });
+        return result;
+    }, {
+        theme,
+        segmentationLayerScopes,
+        segmentationChannelScopesByLayer,
+        segmentationLayerCoordination,
+        segmentationChannelCoordination,
+        obsSegmentationsUrls,
+        obsSegmentationsData,
+        pointLayerScopes,
+        pointLayerCoordination,
+        obsPointsUrls,
+        obsPointsData,
+        pointMultiIndicesData,
+    }, customIsEqualForInitialViewerState);
+    return viewerState;
 }

package/dist-tsc/shader-utils.d.ts

@@ -0,0 +1,126 @@
+/**
+ * Generate a shader for spatialLayerColor encoding with no feature selection.
+ * All points get the static color.
+ * @param {[number, number, number]} staticColor RGB (0-255).
+ * @param {number} opacity Opacity (0-1).
+ * @returns {string} A GLSL shader string.
+ */
+export function getSpatialLayerColorShader(staticColor: [number, number, number], opacity: number): string;
+/**
+ * Generate a shader for spatialLayerColor encoding with feature selection.
+ * Selected features get the static color; unselected get the default color.
+ * @param {[number, number, number]} staticColor RGB (0-255).
+ * @param {number} opacity Opacity (0-1).
+ * @param {number[]} featureIndices Numeric indices of selected features.
+ * @param {[number, number, number]} defaultColor RGB (0-255) for unselected points.
+ * @param {string} featureIndexProp The property name for the feature index in the shader.
+ * @returns {string} A GLSL shader string.
+ */
+export function getSpatialLayerColorWithSelectionShader(staticColor: [number, number, number], opacity: number, featureIndices: number[], defaultColor: [number, number, number], featureIndexProp: string): string;
+/**
+ * Generate a shader for spatialLayerColor encoding with feature selection
+ * and featureFilterMode='featureSelection' (hide unselected points).
+ * @param {[number, number, number]} staticColor RGB (0-255).
+ * @param {number} opacity Opacity (0-1).
+ * @param {number[]} featureIndices Numeric indices of selected features.
+ * @param {string} featureIndexProp The property name for the feature index in the shader.
+ * @returns {string} A GLSL shader string.
+ */
+export function getSpatialLayerColorFilteredShader(staticColor: [number, number, number], opacity: number, featureIndices: number[], featureIndexProp: string): string;
+/**
+ * Generate a shader for geneSelection encoding with no feature selection.
+ * All points get the static color (since no features are selected to
+ * determine per-feature colors).
+ * @param {[number, number, number]} staticColor RGB (0-255).
+ * @param {number} opacity Opacity (0-1).
+ * @returns {string} A GLSL shader string.
+ */
+export function getGeneSelectionNoSelectionShader(staticColor: [number, number, number], opacity: number): string;
+/**
+ * Generate a shader for geneSelection encoding with feature selection.
+ * Each selected feature gets its color from featureColor; unselected
+ * points get the default color.
+ * @param {number[]} featureIndices Numeric indices of selected features.
+ * @param {[number, number, number][]} featureColors RGB (0-255) for each
+ *   selected feature, in the same order as featureIndices.
+ * @param {[number, number, number]} staticColor Fallback RGB (0-255)
+ *   for selected features without a specified color.
+ * @param {[number, number, number]} defaultColor RGB (0-255) for
+ *   unselected points.
+ * @param {number} opacity Opacity (0-1).
+ * @param {string} featureIndexProp The property name for the feature index in the shader.
+ * @returns {string} A GLSL shader string.
+ */
+export function getGeneSelectionWithSelectionShader(featureIndices: number[], featureColors: [number, number, number][], staticColor: [number, number, number], defaultColor: [number, number, number], opacity: number, featureIndexProp: string): string;
+/**
+ * Generate a shader for geneSelection encoding with feature selection
+ * and featureFilterMode='featureSelection' (hide unselected points).
+ * @param {number[]} featureIndices Numeric indices of selected features.
+ * @param {[number, number, number][]} featureColors RGB (0-255) for each
+ *   selected feature.
+ * @param {[number, number, number]} staticColor Fallback RGB (0-255).
+ * @param {number} opacity Opacity (0-1).
+ * @param {string} featureIndexProp The property name for the feature index in the shader.
+ * @returns {string} A GLSL shader string.
+ */
+export function getGeneSelectionFilteredShader(featureIndices: number[], featureColors: [number, number, number][], staticColor: [number, number, number], opacity: number, featureIndexProp: string): string;
+/**
+ * Generate a shader for randomByFeature encoding with no feature selection.
+ * Each feature gets a deterministic color from PALETTE based on its index.
+ * @param {number} opacity Opacity (0-1).
+ * @param {string} featureIndexProp The property name for the feature index in the shader.
+ * @returns {string} A GLSL shader string.
+ */
+export function getRandomByFeatureShader(opacity: number, featureIndexProp: string): string;
+/**
+ * Generate a shader for randomByFeature encoding with feature selection.
+ * Selected features get their deterministic palette color; unselected
+ * points get the default color.
+ * @param {number[]} featureIndices Numeric indices of selected features.
+ * @param {[number, number, number]} defaultColor RGB (0-255) for unselected.
+ * @param {number} opacity Opacity (0-1).
+ * @param {string} featureIndexProp The property name for the feature index in the shader.
+ * @returns {string} A GLSL shader string.
+ */
+export function getRandomByFeatureWithSelectionShader(featureIndices: number[], defaultColor: [number, number, number], opacity: number, featureIndexProp: string): string;
+/**
+ * Generate a shader for randomByFeature encoding with feature selection
+ * and featureFilterMode='featureSelection' (hide unselected points).
+ * @param {number[]} featureIndices Numeric indices of selected features.
+ * @param {number} opacity Opacity (0-1).
+ * @param {string} featureIndexProp The property name for the feature index in the shader.
+ * @returns {string} A GLSL shader string.
+ */
+export function getRandomByFeatureFilteredShader(featureIndices: number[], opacity: number, featureIndexProp: string): string;
+/**
+ * Generate a shader for random-per-point encoding with no feature selection.
+ * Each point gets a pseudo-random color based on its index.
+ * @param {number} opacity Opacity (0-1).
+ * @param {string} featureIndexProp The property name for the feature index in the shader.
+ * @param {string} pointIndexProp The property name for the point index in the shader.
+ * @returns {string} A GLSL shader string.
+ */
+export function getRandomPerPointShader(opacity: number, featureIndexProp: string, pointIndexProp: string): string;
+/**
+ * Generate a shader for random-per-point encoding with feature selection.
+ * Selected points get a pseudo-random color; unselected get the default color.
+ * @param {number[]} featureIndices Numeric indices of selected features.
+ * @param {[number, number, number]} defaultColor RGB (0-255) for unselected.
+ * @param {number} opacity Opacity (0-1).
+ * @param {string} featureIndexProp The property name for the feature index in the shader.
+ * @param {string} pointIndexProp The property name for the point index in the shader.
+ * @returns {string} A GLSL shader string.
+ */
+export function getRandomPerPointWithSelectionShader(featureIndices: number[], defaultColor: [number, number, number], opacity: number, featureIndexProp: string, pointIndexProp: string): string;
+/**
+ * Generate a shader for random-per-point encoding with feature selection
+ * and featureFilterMode='featureSelection' (hide unselected points).
+ * @param {number[]} featureIndices Numeric indices of selected features.
+ * @param {number} opacity Opacity (0-1).
+ * @param {string} featureIndexProp The property name for the feature index in the shader.
+ * @param {string} pointIndexProp The property name for the point index in the shader.
+ * @returns {string} A GLSL shader string.
+ */
+export function getRandomPerPointFilteredShader(featureIndices: number[], opacity: number, featureIndexProp: string, pointIndexProp: string): string;
+export function getPointsShader(layerCoordination: any): string;
+//# sourceMappingURL=shader-utils.d.ts.map

package/dist-tsc/shader-utils.d.ts.map

@@ -0,0 +1 @@
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